Yes, you should be able to do that: edit your permalink settings for the site to make sure they're working and then edit the URL settings for the post-type's in questions. I did some updates to this on the dev branch that will be released in 0.9.7.

I do have to say that I loathe the way WP handles URLs. If you need URL flexibility, I strongly recommend MODx -- it's light-years ahead of WordPress in this area.